AsMamDB: an alternative splice database of mammals. - Hongkai Ji; Qing Zhou; Fang Wen 004; Huiyu Xia; Xin Lu; Yanda Li (Nucleic Acids Res., 2001)

TileMap: create chromosomal map of tiling array hybridizations. - Hongkai Ji; Wing Hung Wong (Bioinform., 2005)

An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse. - Ryung S. Kim; Hongkai Ji; Wing Hung Wong (BMC Bioinform., 2006)

TileProbe: modeling tiling array probe effects using publicly available data. - Jennifer Toolan Judy; Hongkai Ji (Bioinform., 2009)

JAMIE: joint analysis of multiple ChIP-chip experiments. - Hao Wu 003; Hongkai Ji (Bioinform., 2010)

Computational Analysis of ChIP-chip Data. - Hongkai Ji (Handbook of Statistical Bioinformatics, 2011)

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. - Li Chen 029; George Wu; Hongkai Ji (Bioinform., 2011)

iASeq: integrating multiple chip-seq datasets for detecting allele-specific binding. - Yingying Wei; Xia Li; Qianfei Wang; Hongkai Ji (BMC Bioinform., 2012)

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. - George Wu; Jason T. Yustein; Matthew N. McCall; Michael J. Zilliox; Rafael A. Irizarry; Karen Zeller; Chi V. Dang; Hongkai Ji (Bioinform., 2013)

Gene set bagging for estimating the probability a statistically significant result will replicate. - Andrew E. Jaffe; John D. Storey; Hongkai Ji; Jeffrey T. Leek (BMC Bioinform., 2013)

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking. - George Wu; Hongkai Ji (BMC Bioinform., 2013)

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes. - Jie Wang 066; Shuli Xia; Brian Arand; Heng Zhu; Raghu Machiraju; Kun Huang 001; Hongkai Ji; Jiang Qian (PLoS Comput. Biol., 2016)

Single-cell regulome data analysis by SCRAT. - Zhicheng Ji; Weiqiang Zhou; Hongkai Ji (Bioinform., 2017)

Profiling Chromatin Accessibility at Single-cell Resolution. - Sarthak Sinha; Ansuman T. Satpathy; Weiqiang Zhou; Hongkai Ji; Jo A. Stratton; Arzina Jaffer; Nizar Bahlis; Sorana Morrissy; Jeff A. Biernaskie (Genom. Proteom. Bioinform., 2021)

EDClust: an EM-MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing. - Xin Wei; Ziyi Li 001; Hongkai Ji; Hao Wu 003 (Bioinform., 2022)